Contacts of the helix formed by residues 225 - 239 (chain A) in PDB entry 5UC7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A ILE* 3.7 24.5 - - + -
223A TYR 3.8 2.4 - - - +
224A HIS* 1.3 102.4 - - + +
226A GLN* 1.3 64.0 + - - +
227A TRP 3.0 2.2 - - - -
228A LEU* 2.9 15.2 + - - +
229A GLN* 3.2 17.6 + - - +
262A HIS* 3.7 35.2 - - + +
263A ALA* 3.6 4.7 - - + +
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Residues in contact with GLN 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A TRP* 3.6 43.5 - - + -
188A GLU* 5.8 0.2 + - - -
191A MET* 3.7 14.5 - - + +
224A HIS* 2.9 22.5 + - + +
225A PRO* 1.3 77.3 - - - +
227A TRP* 1.3 61.3 + - - +
229A GLN* 3.3 24.4 + - - +
230A ARG* 3.0 33.0 + - - +
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Residues in contact with TRP 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A PHE* 3.6 28.7 - + + -
176A PRO 4.7 4.0 - - - -
178A PRO* 3.2 40.2 + - + -
185A GLU 5.1 0.2 + - - -
186A TRP* 3.5 25.2 - - + +
187A ASP 4.3 4.9 - - - -
190A ASP* 3.4 48.5 - - + -
191A MET* 3.5 30.3 - - + -
194A PHE* 4.2 12.1 - + + -
223A TYR* 3.7 26.0 - + + +
224A HIS 3.2 26.0 + - - +
225A PRO 3.0 0.2 - - - -
226A GLN* 1.3 78.5 - - - +
228A LEU* 1.3 57.0 + - - +
230A ARG* 3.8 1.0 - - - +
231A ILE* 2.9 46.1 + - + +
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Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A LEU* 3.7 36.8 - - + -
212A PRO* 3.6 22.2 - - + -
213A ILE* 4.0 20.4 - - + -
223A TYR* 3.8 17.3 - - + +
225A PRO 2.9 3.6 + - - +
227A TRP* 1.3 76.9 - - - +
229A GLN* 1.3 61.6 + - - +
231A ILE* 4.1 2.8 - - + +
232A ARG* 2.9 32.6 + - - +
242A LEU* 5.2 2.3 - - + +
259A ALA 4.3 0.4 - - - +
260A CYS* 4.2 17.0 - - - -
263A ALA* 3.5 25.6 - - + -
265A ILE* 3.9 17.6 - - + +
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Residues in contact with GLN 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A PRO* 3.2 16.2 + - - +
226A GLN* 3.5 23.1 - - - +
228A LEU* 1.3 74.9 - - - +
230A ARG* 1.3 58.6 + - - +
232A ARG* 3.8 2.3 - - - +
233A GLN* 3.1 26.0 + - - +
262A HIS 4.8 1.4 + - - -
263A ALA* 2.7 40.0 + - + +
265A ILE* 3.7 11.4 - - + -
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Residues in contact with ARG 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A GLU* 2.8 34.2 + - - -
191A MET* 3.4 47.7 + - + +
192A VAL* 4.2 14.6 - - - +
195A ALA* 5.0 6.3 - - - +
226A GLN* 3.0 27.0 + - + +
227A TRP 3.9 2.7 - - - +
229A GLN* 1.3 76.7 - - - +
231A ILE* 1.3 60.2 + - + +
233A GLN* 3.2 24.1 + - - +
234A MET* 2.9 47.8 + - - +
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Residues in contact with ILE 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A PHE* 3.5 33.0 - - + -
191A MET* 5.8 0.2 - - - -
194A PHE* 3.9 29.6 - - + -
208A VAL* 4.0 22.9 - - + -
210A LEU* 3.7 15.0 - - + -
227A TRP* 2.9 32.9 + - + +
228A LEU* 4.1 3.6 - - - +
230A ARG* 1.3 75.6 - - + +
232A ARG* 1.3 59.8 + - - +
234A MET* 3.1 11.0 + - + +
235A CYS* 2.9 34.1 + - - -
242A LEU* 4.1 17.5 - - + -
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Residues in contact with ARG 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A LEU 2.9 19.2 + - - +
229A GLN 3.8 4.3 - - - +
231A ILE* 1.3 78.4 - - - +
233A GLN* 1.3 55.5 + - - +
235A CYS* 3.6 19.6 + - - +
236A ASP* 2.9 56.5 + - - +
240A ILE 3.9 4.4 + - - -
242A LEU* 3.7 25.4 - - + +
265A ILE* 4.0 22.0 - - + -
266A ALA 2.9 30.2 + - - +
267A PRO 3.8 0.2 - - - -
268A ASP* 3.0 41.6 + - - +
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Residues in contact with GLN 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A GLN 3.1 17.7 + - - +
230A ARG* 3.5 26.5 + - - +
231A ILE 3.2 0.2 - - - -
232A ARG* 1.3 74.2 - - - +
234A MET* 1.3 69.3 + - + +
236A ASP* 3.3 11.3 + - - +
237A ARG* 2.9 64.8 + - + +
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Residues in contact with MET 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A MET* 5.0 3.4 - - - +
194A PHE* 3.3 35.4 - - + -
195A ALA* 3.5 33.9 - - + -
198A MET* 3.1 40.9 - - + +
230A ARG* 2.9 38.5 + - + +
231A ILE* 3.5 12.3 - - - +
233A GLN* 1.3 79.7 - - + +
235A CYS* 1.3 62.5 + - - +
237A ARG* 3.1 21.3 + - - +
238A GLU* 3.1 7.8 + - - +
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Residues in contact with CYS 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A MET* 4.0 8.7 - - - -
208A VAL* 3.8 33.4 - - - -
231A ILE* 2.9 25.8 + - - +
232A ARG* 3.6 15.0 - - - +
234A MET* 1.3 76.5 - - - +
236A ASP* 1.3 58.0 + - - +
238A GLU 3.2 1.0 + - - -
239A GLY* 2.8 26.9 + - - -
240A ILE* 3.0 36.8 + - - +
241A LEU 4.2 4.5 - - - -
242A LEU* 4.3 7.2 - - - -
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Residues in contact with ASP 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ARG* 2.9 61.3 + - - +
233A GLN* 3.5 8.7 - - - +
235A CYS* 1.3 75.9 - - - +
237A ARG* 1.3 63.2 + - + +
239A GLY* 3.6 8.0 + - - -
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Residues in contact with ARG 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A GLN* 2.9 56.5 + - + +
234A MET* 3.1 14.6 + - - +
236A ASP* 1.3 76.9 - - + +
238A GLU* 1.3 67.4 + - + +
239A GLY 3.9 0.2 + - - -
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Residues in contact with GLU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A TRP* 5.1 1.4 - - - -
134A ARG* 4.8 9.7 + - - -
198A MET* 3.3 26.7 - - + -
199A ALA* 5.6 2.8 - - - +
202A ARG* 3.0 56.9 + - + +
234A MET 3.1 6.9 + - - +
235A CYS 4.0 0.9 - - - +
237A ARG* 1.3 84.7 - - + +
239A GLY* 1.3 60.2 + - - +
240A ILE* 3.6 26.4 + - + +
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Residues in contact with GLY 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A TYR* 4.6 9.0 + - - -
127A TRP* 3.3 23.9 - - - -
235A CYS 2.8 6.0 + - - -
236A ASP* 3.6 7.0 + - - -
237A ARG 3.5 2.4 - - - -
238A GLU* 1.3 77.9 - - - +
240A ILE* 1.3 64.5 + - - +
241A LEU* 3.8 2.8 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il